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Makwana R, Christ C, Marchi E, Harpell R, Lyon GJ. A Natural History of NAA15-related Neurodevelopmental Disorder Through Adolescence. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.20.24306120. [PMID: 38712024 PMCID: PMC11071585 DOI: 10.1101/2024.04.20.24306120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
NAA15 is a member of the NatA N-terminal acetyltransferase complex which acts by interacting with the NAA10 enzymatic sub-unit. Individuals with variants in the NAA15 coding region develop NAA15-related neurodevelopmental syndrome which presents with a wide array of manifestations that affect the heart, brain, musculoskeletal system, and behavioral and cognitive development. We tracked a cohort of 26 participants (8 females and 18 males) over time, each with a pathogenic NAA15 variant, and administered the Vineland-3 assessment to them to assess their adaptive functioning. We found that the cohort performed significantly worse compared to the normalized Vineland values. On average, females performed better than males across all domains. They performed significantly better on the Motor Domain and Fine Motor Sub-Domain portions of the assessment. Over time, females showed a decrease in adaptive functioning with the decline being especially strongly correlated at the Coping subdomain, Domestic sub-domain, and Fine motor sub-domains. It is difficult to determine the strength of these correlations due to limited power. Males (after excluding one outlier) showed a moderate positive correlation between age and ABC standard score. Ultimately, additional longitudinal data should be collected to determine the validity of the between sex-differences and to better understand the change in adaptive behavioral outcomes of individuals with NAA15-neurodevelopmental disorder as they age.
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Affiliation(s)
- Rikhil Makwana
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
| | - Carolina Christ
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
| | - Elaine Marchi
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
| | - Randie Harpell
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
| | - Gholson J Lyon
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
- George A. Jervis Clinic, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
- Biology PhD Program, The Graduate Center, The City University of New York, New York, United States of America
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2
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Venezian J, Bar-Yosef H, Ben-Arie Zilberman H, Cohen N, Kleifeld O, Fernandez-Recio J, Glaser F, Shiber A. Diverging co-translational protein complex assembly pathways are governed by interface energy distribution. Nat Commun 2024; 15:2638. [PMID: 38528060 DOI: 10.1038/s41467-024-46881-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/12/2024] [Indexed: 03/27/2024] Open
Abstract
Protein-protein interactions are at the heart of all cellular processes, with the ribosome emerging as a platform, orchestrating the nascent-chain interplay dynamics. Here, to study the characteristics governing co-translational protein folding and complex assembly, we combine selective ribosome profiling, imaging, and N-terminomics with all-atoms molecular dynamics. Focusing on conserved N-terminal acetyltransferases (NATs), we uncover diverging co-translational assembly pathways, where highly homologous subunits serve opposite functions. We find that only a few residues serve as "hotspots," initiating co-translational assembly interactions upon exposure at the ribosome exit tunnel. These hotspots are characterized by high binding energy, anchoring the entire interface assembly. Alpha-helices harboring hotspots are highly thermolabile, folding and unfolding during simulations, depending on their partner subunit to avoid misfolding. In vivo hotspot mutations disrupted co-translational complexation, leading to aggregation. Accordingly, conservation analysis reveals that missense NATs variants, causing neurodevelopmental and neurodegenerative diseases, disrupt putative hotspot clusters. Expanding our study to include phosphofructokinase, anthranilate synthase, and nucleoporin subcomplex, we employ AlphaFold-Multimer to model the complexes' complete structures. Computing MD-derived interface energy profiles, we find similar trends. Here, we propose a model based on the distribution of interface energy as a strong predictor of co-translational assembly.
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Affiliation(s)
- Johannes Venezian
- Faculty of Biology, Technion Israel institute of Technology, Haifa, Israel
| | - Hagit Bar-Yosef
- Faculty of Biology, Technion Israel institute of Technology, Haifa, Israel
| | | | - Noam Cohen
- Faculty of Biology, Technion Israel institute of Technology, Haifa, Israel
| | - Oded Kleifeld
- Faculty of Biology, Technion Israel institute of Technology, Haifa, Israel
| | - Juan Fernandez-Recio
- Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC-Universidad de La Rioja-Gobierno de La Rioja, Logroño, Spain
| | - Fabian Glaser
- Lorry I. Lokey Interdisciplinary Center for Life Sciences & Engineering, Haifa, Israel
| | - Ayala Shiber
- Faculty of Biology, Technion Israel institute of Technology, Haifa, Israel.
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Gong X, Boyer JB, Gierlich S, Pożoga M, Weidenhausen J, Sinning I, Meinnel T, Giglione C, Wang Y, Hell R, Wirtz M. HYPK controls stability and catalytic activity of the N-terminal acetyltransferase A in Arabidopsis thaliana. Cell Rep 2024; 43:113768. [PMID: 38363676 DOI: 10.1016/j.celrep.2024.113768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/12/2023] [Accepted: 01/25/2024] [Indexed: 02/18/2024] Open
Abstract
The ribosome-tethered N-terminal acetyltransferase A (NatA) acetylates 52% of soluble proteins in Arabidopsis thaliana. This co-translational modification of the N terminus stabilizes diverse cytosolic plant proteins. The evolutionary conserved Huntingtin yeast partner K (HYPK) facilitates NatA activity in planta, but in vitro, its N-terminal helix α1 inhibits human NatA activity. To dissect the regulatory function of HYPK protein domains in vivo, we genetically engineer CRISPR-Cas9 mutants expressing a HYPK fragment lacking all functional domains (hypk-cr1) or an internally deleted HYPK variant truncating helix α1 but retaining the C-terminal ubiquitin-associated (UBA) domain (hypk-cr2). We find that the UBA domain of HYPK is vital for stabilizing the NatA complex in an organ-specific manner. The N terminus of HYPK, including helix α1, is critical for promoting NatA activity on substrates starting with various amino acids. Consequently, deleting only 42 amino acids inside the HYPK N terminus causes substantial destabilization of the plant proteome and higher tolerance toward drought stress.
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Affiliation(s)
- Xiaodi Gong
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Jean-Baptiste Boyer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Simone Gierlich
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Marlena Pożoga
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | | | - Irmgard Sinning
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Yonghong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, 271018 Tai'an, China
| | - Rüdiger Hell
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Markus Wirtz
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany.
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4
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Abstract
Most proteins receive an acetyl group at the N terminus while in their nascency as the result of modification by co-translationally acting N-terminal acetyltransferases (NATs). The N-terminal acetyl group can influence several aspects of protein functionality. From studies of NAT-lacking cells, it is evident that several cellular processes are affected by this modification. More recently, an increasing number of genetic cases have demonstrated that N-terminal acetylation has crucial roles in human physiology and pathology. In this Cell Science at a Glance and the accompanying poster, we provide an overview of the human NAT enzymes and their properties, substrate coverage, cellular roles and connections to human disease.
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Affiliation(s)
- Henriette Aksnes
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
| | - Nina McTiernan
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
- Department of Biological Sciences, University of Bergen, 5009 Bergen, Norway
- Department of Surgery, Haukeland University Hospital, 5009 Bergen, Norway
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5
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Deng S, Gardner SM, Gottlieb L, Pan B, Petersson EJ, Marmorstein R. Molecular role of NAA38 in thermostability and catalytic activity of the human NatC N-terminal acetyltransferase. Structure 2023; 31:166-173.e4. [PMID: 36638802 PMCID: PMC9898148 DOI: 10.1016/j.str.2022.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 11/22/2022] [Accepted: 12/15/2022] [Indexed: 01/15/2023]
Abstract
N-terminal acetylation occurs on over 80% of human proteins and is catalyzed by a family of N-terminal acetyltransferases (NATs). All NATs contain a small catalytic subunit, while some also contain a large auxiliary subunit that facilitates catalysis and ribosome targeting for co-translational acetylation. NatC is one of the major NATs containing an NAA30 catalytic subunit, but uniquely contains two auxiliary subunits, large NAA35 and small NAA38. Here, we report the cryo-EM structures of human NatC (hNatC) complexes with and without NAA38, together with biochemical studies, to reveal that NAA38 increases the thermostability and broadens the substrate-specificity profile of NatC by ordering an N-terminal segment of NAA35 and reorienting an NAA30 N-terminal peptide binding loop for optimal catalysis, respectively. We also note important differences in engagement with a stabilizing inositol hexaphosphate molecule between human and yeast NatC. These studies provide new insights for the function and evolution of the NatC complex.
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Affiliation(s)
- Sunbin Deng
- Department of Chemistry, University of Pennsylvania, 231 South 34(th) Street, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah M Gardner
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Leah Gottlieb
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Buyan Pan
- Department of Chemistry, University of Pennsylvania, 231 South 34(th) Street, Philadelphia, PA 19104, USA
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, 231 South 34(th) Street, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Ronen Marmorstein
- Department of Chemistry, University of Pennsylvania, 231 South 34(th) Street, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA.
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6
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Van Damme P, Osberg C, Jonckheere V, Glomnes N, Gevaert K, Arnesen T, Aksnes H. Expanded in vivo substrate profile of the yeast N-terminal acetyltransferase NatC. J Biol Chem 2023; 299:102824. [PMID: 36567016 PMCID: PMC9867985 DOI: 10.1016/j.jbc.2022.102824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/05/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
N-terminal acetylation is a conserved protein modification among eukaryotes. The yeast Saccharomyces cerevisiae is a valuable model system for studying this modification. The bulk of protein N-terminal acetylation in S. cerevisiae is catalyzed by the N-terminal acetyltransferases NatA, NatB, and NatC. Thus far, proteome-wide identification of the in vivo protein substrates of yeast NatA and NatB has been performed by N-terminomics. Here, we used S. cerevisiae deleted for the NatC catalytic subunit Naa30 and identified 57 yeast NatC substrates by N-terminal combined fractional diagonal chromatography analysis. Interestingly, in addition to the canonical N-termini starting with ML, MI, MF, and MW, yeast NatC substrates also included MY, MK, MM, MA, MV, and MS. However, for some of these substrate types, such as MY, MK, MV, and MS, we also uncovered (residual) non-NatC NAT activity, most likely due to the previously established redundancy between yeast NatC and NatE/Naa50. Thus, we have revealed a complex interplay between different NATs in targeting methionine-starting N-termini in yeast. Furthermore, our results showed that ectopic expression of human NAA30 rescued known NatC phenotypes in naa30Δ yeast, as well as partially restored the yeast NatC Nt-acetylome. Thus, we demonstrate an evolutionary conservation of NatC from yeast to human thereby underpinning future disease models to study pathogenic NAA30 variants. Overall, this work offers increased biochemical and functional insights into NatC-mediated N-terminal acetylation and provides a basis for future work to pinpoint the specific molecular mechanisms that link the lack of NatC-mediated N-terminal acetylation to phenotypes of NatC deletion yeast.
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Affiliation(s)
- Petra Van Damme
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
| | - Camilla Osberg
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Veronique Jonckheere
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Nina Glomnes
- Department of Biomedicine, University of Bergen, Bergen, Norway; Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway; Department of Biological Sciences, University of Bergen, Bergen, Norway; Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - Henriette Aksnes
- Department of Biomedicine, University of Bergen, Bergen, Norway.
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Fang T, Wang D, Li R, Yu W, Tian H. Pan-cancer analysis reveals NAA50 as a cancer prognosis and immune infiltration-related biomarker. Front Genet 2022; 13:1035337. [PMID: 36568377 PMCID: PMC9782403 DOI: 10.3389/fgene.2022.1035337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
Background: N-Alpha-Acetyltransferase 50 (NAA50) has acetyltransferase activity and is important for chromosome segregation. However, the function and mechanism of NAA50 expression in cancer development was still unclear. Here, we systematically researched the function and mechanism of NAA50 in pan-cancer, and further verified the results of NAA50 in lung adenocarcinoma (LUAD). Methods: In this study, using the online databases TIMER2.0, SangerBox3.0, HPA, UCSC, GEPIA, cBioPortal, UALCAN, TISIDB, CancerSEA and LinkedOmics, we focused on the relevance between NAA50 and oncogenesis, progression, methylation, immune infiltration, function and prognosis. In addition, the proliferation of cells was detected by CCK-8 and Edu assay. Finally, we analyzed the relationship between the expression of NAA50 and cell cycle related proteins. Results: Pan-cancer analysis indicated that NAA50 was overexpressed in most cancers. And there was a significant correlation between NAA50 expression and the prognosis of cancer patients. In the meantime, NAA50 gene changes occur in a variety of tumors. Compared with normal tissues, the methylation level of NAA50 promoter increased in most cancer tissues. In addition, the results exhibited that in most cancers, NAA50 was significantly positively correlated with bone myeloid-derived suppressor cell (MDSC) infiltration and negatively correlated with T cell NK infiltration. Moreover, functional enrichment indicated that NAA50 regulates cell cycle and proliferation in LUAD. In vitro experiments testified that knockout of NAA50 could significantly inhibit the proliferation of LUAD. Conclusion: NAA50 may be a potential biomarker and oncogene of pan-cancer, especially LUAD, which may promote the occurrence and development of tumors through different mechanisms. Furthermore, NAA50 was bound up with to immune cell infiltration in pan-cancer, meaning NAA50 may be an important therapeutic target for human cancers.
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8
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Weidenhausen J, Kopp J, Ruger-Herreros C, Stein F, Haberkant P, Lapouge K, Sinning I. Extended N-Terminal Acetyltransferase Naa50 in Filamentous Fungi Adds to Naa50 Diversity. Int J Mol Sci 2022; 23:ijms231810805. [PMID: 36142717 PMCID: PMC9500918 DOI: 10.3390/ijms231810805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Most eukaryotic proteins are N-terminally acetylated by a set of Nα acetyltransferases (NATs). This ancient and ubiquitous modification plays a fundamental role in protein homeostasis, while mutations are linked to human diseases and phenotypic defects. In particular, Naa50 features species-specific differences, as it is inactive in yeast but active in higher eukaryotes. Together with NatA, it engages in NatE complex formation for cotranslational acetylation. Here, we report Naa50 homologs from the filamentous fungi Chaetomium thermophilum and Neurospora crassa with significant N- and C-terminal extensions to the conserved GNAT domain. Structural and biochemical analyses show that CtNaa50 shares the GNAT structure and substrate specificity with other homologs. However, in contrast to previously analyzed Naa50 proteins, it does not form NatE. The elongated N-terminus increases Naa50 thermostability and binds to dynein light chain protein 1, while our data suggest that conserved positive patches in the C-terminus allow for ribosome binding independent of NatA. Our study provides new insights into the many facets of Naa50 and highlights the diversification of NATs during evolution.
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Affiliation(s)
- Jonas Weidenhausen
- Heidelberg University Biochemistry Center (BZH), 69120 Heidelberg, Germany
| | - Jürgen Kopp
- Heidelberg University Biochemistry Center (BZH), 69120 Heidelberg, Germany
| | - Carmen Ruger-Herreros
- Heidelberg University Biochemistry Center (BZH), 69120 Heidelberg, Germany
- Center for Molecular Biology of the University of Heidelberg (ZMBH), 69120 Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, 69117 Heidelberg, Germany
| | - Per Haberkant
- Proteomics Core Facility, EMBL Heidelberg, 69117 Heidelberg, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Center (BZH), 69120 Heidelberg, Germany
- Protein Expression and Purification Core Facility, EMBL Heidelberg, 69117 Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), 69120 Heidelberg, Germany
- Correspondence:
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Parenti I, Kaiser FJ. Cornelia de Lange Syndrome as Paradigm of Chromatinopathies. Front Neurosci 2021; 15:774950. [PMID: 34803598 PMCID: PMC8603810 DOI: 10.3389/fnins.2021.774950] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/18/2021] [Indexed: 12/18/2022] Open
Abstract
Chromatinopathies can be defined as a class of neurodevelopmental disorders caused by mutations affecting proteins responsible for chromatin remodeling and transcriptional regulation. The resulting dysregulation of gene expression favors the onset of a series of clinical features such as developmental delay, intellectual disability, facial dysmorphism, and behavioral disturbances. Cornelia de Lange syndrome (CdLS) is a prime example of a chromatinopathy. It is caused by mutations affecting subunits or regulators of the cohesin complex, a multisubunit protein complex involved in various molecular mechanisms such as sister chromatid cohesion, transcriptional regulation and formation of topologically associated domains. However, disease-causing variants in non-cohesin genes with overlapping functions have also been described in association with CdLS. Notably, the majority of these genes had been previously found responsible for distinct neurodevelopmental disorders that also fall within the category of chromatinopathies and are frequently considered as differential diagnosis for CdLS. In this review, we provide a systematic overview of the current literature to summarize all mutations in non-cohesin genes identified in association with CdLS phenotypes and discuss about the interconnection of proteins belonging to the chromatinopathies network.
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Affiliation(s)
- Ilaria Parenti
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Frank J Kaiser
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany.,Essener Zentrum für Seltene Erkrankungen (EZSE), Universitätsklinikum Essen, Essen, Germany
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10
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Van Damme P. Charting the N-Terminal Acetylome: A Comprehensive Map of Human NatA Substrates. Int J Mol Sci 2021; 22:ijms221910692. [PMID: 34639033 PMCID: PMC8509067 DOI: 10.3390/ijms221910692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/10/2021] [Accepted: 09/29/2021] [Indexed: 11/29/2022] Open
Abstract
N-terminal acetylation (Nt-acetylation) catalyzed by conserved N-terminal acetyltransferases or NATs embodies a modification with one of the highest stoichiometries reported for eukaryotic protein modifications to date. Comprising the catalytic N-alpha acetyltransferase (NAA) subunit NAA10 plus the ribosome anchoring regulatory subunit NAA15, NatA represents the major acetyltransferase complex with up to 50% of all mammalian proteins representing potential substrates. Largely in consequence of the essential nature of NatA and its high enzymatic activity, its experimentally confirmed mammalian substrate repertoire remained poorly charted. In this study, human NatA knockdown conditions achieving near complete depletion of NAA10 and NAA15 expression resulted in lowered Nt-acetylation of over 25% out of all putative NatA targets identified, representing an up to 10-fold increase in the reported number of substrate N-termini affected upon human NatA perturbation. Besides pointing to less efficient NatA substrates being prime targets, several putative NatE substrates were shown to be affected upon human NatA knockdown. Intriguingly, next to a lowered expression of ribosomal proteins and proteins constituting the eukaryotic 48S preinitiation complex, steady-state levels of protein N-termini additionally point to NatA Nt-acetylation deficiency directly impacting protein stability of knockdown affected targets.
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Affiliation(s)
- Petra Van Damme
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
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11
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Deng Y, Deng S, Ho YH, Gardner SM, Huang Z, Marmorstein R, Huang R. Novel Bisubstrate Inhibitors for Protein N-Terminal Acetyltransferase D. J Med Chem 2021; 64:8263-8271. [PMID: 34110812 PMCID: PMC8392721 DOI: 10.1021/acs.jmedchem.1c00141] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein N-terminal acetyltransferase D (NatD, NAA40) that specifically acetylates the alpha-N-terminus of histone H4 and H2A has been implicated in various diseases, but no inhibitor has been reported for this important enzyme. Based on the acetyl transfer mechanism of NatD, we designed and prepared a series of highly potent NatD bisubstrate inhibitors by covalently linking coenzyme A to different peptide substrates via an acetyl or propionyl spacer. The most potent bisubstrate inhibitor displayed an apparent Ki value of 1.0 nM. Biochemical studies indicated that bisubstrate inhibitors are competitive to the peptide substrate and noncompetitive to the cofactor, suggesting that NatD undergoes an ordered Bi-Bi mechanism. We also demonstrated that these inhibitors are highly specific toward NatD, displaying about 1000-fold selectivity over other closely related acetyltransferases. High-resolution crystal structures of NatD bound to two of these inhibitors revealed the molecular basis for their selectivity and inhibition mechanism, providing a rational path for future inhibitor development.
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Affiliation(s)
- Youchao Deng
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Sunbin Deng
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yi-Hsun Ho
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Sarah M. Gardner
- Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Zhi Huang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ronen Marmorstein
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Rong Huang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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12
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Deng S, Gottlieb L, Pan B, Supplee J, Wei X, Petersson EJ, Marmorstein R. Molecular mechanism of N-terminal acetylation by the ternary NatC complex. Structure 2021; 29:1094-1104.e4. [PMID: 34019809 DOI: 10.1016/j.str.2021.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/15/2021] [Accepted: 04/30/2021] [Indexed: 11/30/2022]
Abstract
Protein N-terminal acetylation is predominantly a ribosome-associated modification, with NatA-E serving as the major enzymes. NatC is the most unusual of these enzymes, containing one Naa30 catalytic subunit and two auxiliary subunits, Naa35 and Naa38; and substrate selectivity profile that overlaps with NatE. Here, we report the cryoelectron microscopy structure of S. pombe NatC with a NatE/C-type bisubstrate analog and inositol hexaphosphate (IP6), and associated biochemistry studies. We find that the presence of three subunits is a prerequisite for normal NatC acetylation activity in yeast and that IP6 binds tightly to NatC to stabilize the complex. We also describe the molecular basis for IP6-mediated NatC complex stabilization and the overlapping yet distinct substrate profiles of NatC and NatE.
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Affiliation(s)
- Sunbin Deng
- Department of Chemistry, 231 South 34(th) Street, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leah Gottlieb
- Department of Chemistry, 231 South 34(th) Street, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Buyan Pan
- Department of Chemistry, 231 South 34(th) Street, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Julianna Supplee
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Xuepeng Wei
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - E James Petersson
- Department of Chemistry, 231 South 34(th) Street, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ronen Marmorstein
- Department of Chemistry, 231 South 34(th) Street, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA.
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13
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Giglione C, Meinnel T. Evolution-Driven Versatility of N Terminal Acetylation in Photoautotrophs. TRENDS IN PLANT SCIENCE 2021; 26:375-391. [PMID: 33384262 DOI: 10.1016/j.tplants.2020.11.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 10/27/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
N terminal protein α-acetylation (NTA) is a pervasive protein modification that has recently attracted renewed interest. Early studies on NTA were mostly conducted in yeast and metazoans, providing a detailed portrait of the modification, which was indirectly applied to all eukaryotes. However, new findings originating from photosynthetic organisms have expanded our knowledge of this modification, revealing strong similarities as well as idiosyncratic features. Here, we review the most recent advances on NTA and its dedicated machinery in photosynthetic organisms. We discuss the cytosolic and unique plastid NTA machineries and their critical biological roles in development, stress responses, protein translocation, and stability. These new findings suggest that the multitasking plastid and cytosolic machineries evolved to support the specific needs of photoautotrophs.
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Affiliation(s)
- Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
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14
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Ward T, Tai W, Morton S, Impens F, Van Damme P, Van Haver D, Timmerman E, Venturini G, Zhang K, Jang MY, Willcox JAL, Haghighi A, Gelb BD, Chung WK, Goldmuntz E, Porter GA, Lifton RP, Brueckner M, Yost HJ, Bruneau BG, Gorham J, Kim Y, Pereira A, Homsy J, Benson CC, DePalma SR, Varland S, Chen CS, Arnesen T, Gevaert K, Seidman C, Seidman JG. Mechanisms of Congenital Heart Disease Caused by NAA15 Haploinsufficiency. Circ Res 2021; 128:1156-1169. [PMID: 33557580 PMCID: PMC8048381 DOI: 10.1161/circresaha.120.316966] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Tarsha Ward
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Warren Tai
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Sarah Morton
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School.,Division of Newborn Medicine, Boston Children's Hospital (S.M.)
| | - Francis Impens
- VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium (F.I., D.V.H., E.T., K.G.).,VIB Proteomics Core, B-9000 Ghent, Belgium (F.I., D.V.H., E.T.).,Biomolecular Medicine (F.I., D.V.H., E.T., K.G.), Ghent University, B-9000 Ghent, Belgium
| | - Petra Van Damme
- Biochemistry and Microbiology (P.V.D.), Ghent University, B-9000 Ghent, Belgium
| | - Delphi Van Haver
- VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium (F.I., D.V.H., E.T., K.G.).,VIB Proteomics Core, B-9000 Ghent, Belgium (F.I., D.V.H., E.T.).,Biomolecular Medicine (F.I., D.V.H., E.T., K.G.), Ghent University, B-9000 Ghent, Belgium
| | - Evy Timmerman
- VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium (F.I., D.V.H., E.T., K.G.).,VIB Proteomics Core, B-9000 Ghent, Belgium (F.I., D.V.H., E.T.).,Biomolecular Medicine (F.I., D.V.H., E.T., K.G.), Ghent University, B-9000 Ghent, Belgium
| | - Gabriela Venturini
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School.,University of Sao Paulo (G.V.)
| | - Kehan Zhang
- Biomedical Engineering, Boston University, MA (K.Z., C.S.C.).,The Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA (K.Z., C.S.C.)
| | - Min Young Jang
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Jon A L Willcox
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Alireza Haghighi
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School.,Howard Hughes Medical Institute (A.H., C.S.), Harvard Medical School.,Medicine, Brigham and Women's Hospital (A.H., C.S.)
| | - Bruce D Gelb
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York (B.D.G.)
| | - Wendy K Chung
- Pediatrics and Medicine, Columbia University Medical Center, New York (W.K.C.)
| | - Elizabeth Goldmuntz
- Cardiology, Children's Hospital of Philadelphia, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia (E.G.)
| | | | - Richard P Lifton
- Genetics, Yale University School of Medicine, New Haven (R.P.L., M.B.).,Laboratory of Human Genetics and Genomics, Rockefeller University, New York (R.P.L.)
| | - Martina Brueckner
- Genetics, Yale University School of Medicine, New Haven (R.P.L., M.B.).,Pediatrics, Yale University School of Medicine, New Haven (M.B.)
| | - H Joseph Yost
- Molecular Medicine Program, University of Utah, Salt Lake City (H.J.Y.)
| | | | - Joshua Gorham
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Yuri Kim
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School.,Division of Cardiovascular Medicine, Brigham and Women's Hospital (Y.K.)
| | - Alexandre Pereira
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Jason Homsy
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Craig C Benson
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Steven R DePalma
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Sylvia Varland
- Biomedicine (S.V., T.A.), University of Bergen, N-5020 Bergen, Norway.,Biological Sciences (S.V., T.A.), University of Bergen, N-5020 Bergen, Norway.,Donnelly Centre for Cellular and Biomolecular Research, Toronto, Canada (S.V.)
| | - Christopher S Chen
- Biomedical Engineering, Boston University, MA (K.Z., C.S.C.).,The Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA (K.Z., C.S.C.)
| | - Thomas Arnesen
- Biomedicine (S.V., T.A.), University of Bergen, N-5020 Bergen, Norway.,Biological Sciences (S.V., T.A.), University of Bergen, N-5020 Bergen, Norway.,Surgery, Haukeland University Hospital, N-5021 Bergen, Norway (T.A.)
| | - Kris Gevaert
- Biomolecular Medicine (F.I., D.V.H., E.T., K.G.), Ghent University, B-9000 Ghent, Belgium
| | - Christine Seidman
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School.,Howard Hughes Medical Institute (A.H., C.S.), Harvard Medical School.,Medicine, Brigham and Women's Hospital (A.H., C.S.)
| | - J G Seidman
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
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15
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Jing Y, Montano JL, Levy M, Lopez JE, Kung PP, Richardson P, Krajewski K, Florens L, Washburn MP, Meier JL. Harnessing Ionic Selectivity in Acetyltransferase Chemoproteomic Probes. ACS Chem Biol 2021; 16:27-34. [PMID: 33373188 PMCID: PMC9093059 DOI: 10.1021/acschembio.0c00766] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Chemical proteomics provides a powerful strategy for the high-throughput assignment of enzyme function or inhibitor selectivity. However, identifying optimized probes for an enzyme family member of interest and differentiating signal from the background remain persistent challenges in the field. To address this obstacle, here we report a physiochemical discernment strategy for optimizing chemical proteomics based on the coenzyme A (CoA) cofactor. First, we synthesize a pair of CoA-based sepharose pulldown resins differentiated by a single negatively charged residue and find this change alters their capture properties in gel-based profiling experiments. Next, we integrate these probes with quantitative proteomics and benchmark analysis of "probe selectivity" versus traditional "competitive chemical proteomics." This reveals that the former is well-suited for the identification of optimized pulldown probes for specific enzyme family members, while the latter may have advantages in discovery applications. Finally, we apply our anionic CoA pulldown probe to evaluate the selectivity of a recently reported small molecule N-terminal acetyltransferase inhibitor. These studies further validate the use of physical discriminant strategies in chemoproteomic hit identification and demonstrate how CoA-based chemoproteomic probes can be used to evaluate the selectivity of small molecule protein acetyltransferase inhibitors, an emerging class of preclinical therapeutic agents.
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Affiliation(s)
- Yihang Jing
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Jose L Montano
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Michaella Levy
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, United States
| | - Jeffrey E Lopez
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Pei-Pei Kung
- Worldwide Research and Development, Pfizer Inc., San Diego, California 92121, United States
| | - Paul Richardson
- Worldwide Research and Development, Pfizer Inc., San Diego, California 92121, United States
| | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, The University of North Carolina, Chapel Hill, North Carolina 27514, United States
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, United States
| | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, United States
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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16
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Structural basis of Naa20 activity towards a canonical NatB substrate. Commun Biol 2021; 4:2. [PMID: 33398031 PMCID: PMC7782713 DOI: 10.1038/s42003-020-01546-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/30/2020] [Indexed: 01/29/2023] Open
Abstract
N-terminal acetylation is one of the most common protein modifications in eukaryotes and is carried out by N-terminal acetyltransferases (NATs). It plays important roles in protein homeostasis, localization, and interactions and is linked to various human diseases. NatB, one of the major co-translationally active NATs, is composed of the catalytic subunit Naa20 and the auxiliary subunit Naa25, and acetylates about 20% of the proteome. Here we show that NatB substrate specificity and catalytic mechanism are conserved among eukaryotes, and that Naa20 alone is able to acetylate NatB substrates in vitro. We show that Naa25 increases the Naa20 substrate affinity, and identify residues important for peptide binding and acetylation activity. We present the first Naa20 crystal structure in complex with the competitive inhibitor CoA-Ac-MDEL. Our findings demonstrate how Naa20 binds its substrates in the absence of Naa25 and support prospective endeavors to derive specific NAT inhibitors for drug development.
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17
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Weidenhausen J, Kopp J, Armbruster L, Wirtz M, Lapouge K, Sinning I. Structural and functional characterization of the N-terminal acetyltransferase Naa50. Structure 2021; 29:413-425.e5. [PMID: 33400917 DOI: 10.1016/j.str.2020.12.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/28/2020] [Accepted: 12/08/2020] [Indexed: 10/22/2022]
Abstract
The majority of eukaryotic proteins is modified by N-terminal acetylation, which plays a fundamental role in protein homeostasis, localization, and complex formation. N-terminal acetyltransferases (NATs) mainly act co-translationally on newly synthesized proteins at the ribosomal tunnel exit. NatA is the major NAT consisting of Naa10 catalytic and Naa15 auxiliary subunits, and with Naa50 forms the NatE complex. Naa50 has recently been identified in Arabidopsis thaliana and is important for plant development and stress response regulation. Here, we determined high-resolution X-ray crystal structures of AtNaa50 in complex with AcCoA and a bisubstrate analog. We characterized its substrate specificity, determined its enzymatic parameters, and identified functionally important residues. Even though Naa50 is conserved among species, we highlight differences between Arabidopsis and yeast, where Naa50 is catalytically inactive but binds CoA conjugates. Our study provides insights into Naa50 conservation, species-specific adaptations, and serves as a basis for further studies of NATs in plants.
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Affiliation(s)
| | - Jürgen Kopp
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Laura Armbruster
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Markus Wirtz
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany.
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18
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Krtenic B, Drazic A, Arnesen T, Reuter N. Classification and phylogeny for the annotation of novel eukaryotic GNAT acetyltransferases. PLoS Comput Biol 2020; 16:e1007988. [PMID: 33362253 PMCID: PMC7790372 DOI: 10.1371/journal.pcbi.1007988] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 01/07/2021] [Accepted: 10/16/2020] [Indexed: 11/19/2022] Open
Abstract
The enzymes of the GCN5-related N-acetyltransferase (GNAT) superfamily count more than 870 000 members through all kingdoms of life and share the same structural fold. GNAT enzymes transfer an acyl moiety from acyl coenzyme A to a wide range of substrates including aminoglycosides, serotonin, glucosamine-6-phosphate, protein N-termini and lysine residues of histones and other proteins. The GNAT subtype of protein N-terminal acetyltransferases (NATs) alone targets a majority of all eukaryotic proteins stressing the omnipresence of the GNAT enzymes. Despite the highly conserved GNAT fold, sequence similarity is quite low between members of this superfamily even when substrates are similar. Furthermore, this superfamily is phylogenetically not well characterized. Thus functional annotation based on sequence similarity is unreliable and strongly hampered for thousands of GNAT members that remain biochemically uncharacterized. Here we used sequence similarity networks to map the sequence space and propose a new classification for eukaryotic GNAT acetyltransferases. Using the new classification, we built a phylogenetic tree, representing the entire GNAT acetyltransferase superfamily. Our results show that protein NATs have evolved more than once on the GNAT acetylation scaffold. We use our classification to predict the function of uncharacterized sequences and verify by in vitro protein assays that two fungal genes encode NAT enzymes targeting specific protein N-terminal sequences, showing that even slight changes on the GNAT fold can lead to change in substrate specificity. In addition to providing a new map of the relationship between eukaryotic acetyltransferases the classification proposed constitutes a tool to improve functional annotation of GNAT acetyltransferases. Enzymes of the GCN5-related N-acetyltransferase (GNAT) superfamily transfer an acetyl group from one molecule to another. This reaction is called acetylation and is one of the most common reactions inside the cell. The GNAT superfamily counts more than 870 000 members through all kingdoms of life. Despite sharing the same fold the GNAT superfamily is very diverse in terms of amino acid sequence and substrates. The eight N-terminal acetyltransferases (NatA, NatB, etc.. to NatH) are a GNAT subtype which acetylates the free amine group of polypeptide chains. This modification is called N-terminal acetylation and is one of the most abundant protein modifications in eukaryotic cells. This subtype is also characterized by a high sequence diversity even though they share the same substrate. In addition, the phylogeny of the superfamily is not characterized. This hampers functional annotation based on sequence similarity, and discovery of novel NATs. In this work we set out to solve the problem of the classification of eukaryotic GCN5-related acetyltransferases and report the first classification framework of the superfamily. This framework can be used as a tool for annotation of all GCN5-related acetyltransferases. As an example of what can be achieved we report in this paper the computational prediction and in vitro verification of the function of two previously uncharacterized N-terminal acetyltransferases. We also report the first acetyltransferase phylogenetic tree of the GCN5 superfamily. It indicates that N-terminal acetyltransferases do not constitute one homogeneous protein family, but that the ability to bind and acetylate protein N-termini had evolved more than once on the same acetylation scaffold. We also show that even small changes in key positions can lead to altered enzyme specificity.
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Affiliation(s)
- Bojan Krtenic
- Department of Biological Sciences, University of Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Norway
- * E-mail: (BK); (NR)
| | - Adrian Drazic
- Department of Biomedicine, University of Bergen, Norway
| | - Thomas Arnesen
- Department of Biological Sciences, University of Bergen, Norway
- Department of Biomedicine, University of Bergen, Norway
- Department of Surgery, Haukeland University Hospital, Norway
| | - Nathalie Reuter
- Computational Biology Unit, Department of Informatics, University of Bergen, Norway
- Department of Chemistry, University of Bergen, Norway
- * E-mail: (BK); (NR)
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19
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Grunwald S, Hopf LVM, Bock-Bierbaum T, Lally CCM, Spahn CMT, Daumke O. Divergent architecture of the heterotrimeric NatC complex explains N-terminal acetylation of cognate substrates. Nat Commun 2020; 11:5506. [PMID: 33139728 PMCID: PMC7608589 DOI: 10.1038/s41467-020-19321-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 10/06/2020] [Indexed: 02/07/2023] Open
Abstract
The heterotrimeric NatC complex, comprising the catalytic Naa30 and the two auxiliary subunits Naa35 and Naa38, co-translationally acetylates the N-termini of numerous eukaryotic target proteins. Despite its unique subunit composition, its essential role for many aspects of cellular function and its suggested involvement in disease, structure and mechanism of NatC have remained unknown. Here, we present the crystal structure of the Saccharomyces cerevisiae NatC complex, which exhibits a strikingly different architecture compared to previously described N-terminal acetyltransferase (NAT) complexes. Cofactor and ligand-bound structures reveal how the first four amino acids of cognate substrates are recognized at the Naa30–Naa35 interface. A sequence-specific, ligand-induced conformational change in Naa30 enables efficient acetylation. Based on detailed structure–function studies, we suggest a catalytic mechanism and identify a ribosome-binding patch in an elongated tip region of NatC. Our study reveals how NAT machineries have divergently evolved to N-terminally acetylate specific subsets of target proteins. The conserved eukaryotic heterotrimeric NatC complex co-translationally acetylates the N-termini of numerous target proteins. Here, the authors provide insights into the catalytic mechanism of NatC by determining the crystal structures of Saccharomyces cerevisiae NatC in the absence and presence of cofactors and peptide substrates and reveal the molecular basis of substrate binding by further biochemical analyses.
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Affiliation(s)
- Stephan Grunwald
- Department of Crystallography, Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany
| | - Linus V M Hopf
- Department of Crystallography, Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany
| | - Tobias Bock-Bierbaum
- Department of Crystallography, Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
| | - Ciara C M Lally
- Institute of Medical Physics and Biophysics, Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Christian M T Spahn
- Institute of Medical Physics and Biophysics, Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Oliver Daumke
- Department of Crystallography, Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany. .,Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany.
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20
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Ritter A, Berger JH, Deardorff M, Izumi K, Lin KY, Medne L, Ahrens-Nicklas RC. Variants in NAA15 cause pediatric hypertrophic cardiomyopathy. Am J Med Genet A 2020; 185:228-233. [PMID: 33103328 DOI: 10.1002/ajmg.a.61928] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/01/2020] [Accepted: 10/04/2020] [Indexed: 01/28/2023]
Abstract
The NatA N-acetyltransferase complex is important for cotranslational protein modification and regulation of multiple cellular processes. The NatA complex includes the core components of NAA10, the catalytic subunit, and NAA15, the auxiliary component. Both NAA10 and NAA15 have been associated with neurodevelopmental disorders with overlapping clinical features, including variable intellectual disability, dysmorphic facial features, and, less commonly, congenital anomalies such as cleft lip or palate. Cardiac arrhythmias, including long QT syndrome, ventricular tachycardia, and ventricular fibrillation were among the first reported cardiac manifestations in patients with NAA10-related syndrome. Recently, three individuals with NAA10-related syndrome have been reported to also have hypertrophic cardiomyopathy (HCM). The general and cardiac phenotypes of NAA15-related syndrome are not as well described as NAA10-related syndrome. Congenital heart disease, including ventricular septal defects, and arrhythmias, such as ectopic atrial tachycardia, have been reported in a small proportion of patients with NAA15-related syndrome. Given the relationship between NAA10 and NAA15, we propose that HCM is also likely to occur in NAA15-related disorder. We present two patients with pediatric HCM found to have NAA15-related disorder via exome sequencing, providing the first evidence that variants in NAA15 can cause HCM.
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Affiliation(s)
- Alyssa Ritter
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Divison of Cardiology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Justin H Berger
- Divison of Cardiology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Matthew Deardorff
- Department of Pathology and Laboratory Medicine and Pediatrics, Children's Hospital Los Angeles, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Kosuke Izumi
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kimberly Y Lin
- Divison of Cardiology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Livija Medne
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Rebecca C Ahrens-Nicklas
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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21
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Linster E, Layer D, Bienvenut WV, Dinh TV, Weyer FA, Leemhuis W, Brünje A, Hoffrichter M, Miklankova P, Kopp J, Lapouge K, Sindlinger J, Schwarzer D, Meinnel T, Finkemeier I, Giglione C, Hell R, Sinning I, Wirtz M. The Arabidopsis N α -acetyltransferase NAA60 locates to the plasma membrane and is vital for the high salt stress response. THE NEW PHYTOLOGIST 2020; 228:554-569. [PMID: 32548857 DOI: 10.1111/nph.16747] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 05/13/2020] [Indexed: 06/11/2023]
Abstract
In humans and plants, N-terminal acetylation plays a central role in protein homeostasis, affects 80% of proteins in the cytoplasm and is catalyzed by five ribosome-associated N-acetyltransferases (NatA-E). Humans also possess a Golgi-associated NatF (HsNAA60) that is essential for Golgi integrity. Remarkably, NAA60 is absent in fungi and has not been identified in plants. Here we identify and characterize the first plasma membrane-anchored post-translationally acting N-acetyltransferase AtNAA60 in the reference plant Arabidopsis thaliana by the combined application of reverse genetics, global proteomics, live-cell imaging, microscale thermophoresis, circular dichroism spectroscopy, nano-differential scanning fluorometry, intrinsic tryptophan fluorescence and X-ray crystallography. We demonstrate that AtNAA60, like HsNAA60, is membrane-localized in vivo by an α-helical membrane anchor at its C-terminus, but in contrast to HsNAA60, AtNAA60 localizes to the plasma membrane. The AtNAA60 crystal structure provides insights into substrate-binding, the broad substrate specificity and the catalytic mechanism probed by structure-based mutagenesis. Characterization of the NAA60 loss-of-function mutants (naa60-1 and naa60-2) uncovers a plasma membrane-localized substrate of AtNAA60 and the importance of NAA60 during high salt stress. Our findings provide evidence for the plant-specific evolution of a plasma membrane-anchored N-acetyltransferase that is vital for adaptation to stress.
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Affiliation(s)
- Eric Linster
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Dominik Layer
- Heidelberg University Biochemistry Center, Heidelberg, 69120, Germany
| | - Willy V Bienvenut
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, Gif-sur-Yvette Cedex, 91198, France
| | - Trinh V Dinh
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Felix A Weyer
- Heidelberg University Biochemistry Center, Heidelberg, 69120, Germany
| | - Wiebke Leemhuis
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Annika Brünje
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Muenster, Münster, 48149, Germany
| | - Marion Hoffrichter
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Pavlina Miklankova
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Jürgen Kopp
- Heidelberg University Biochemistry Center, Heidelberg, 69120, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Center, Heidelberg, 69120, Germany
| | - Julia Sindlinger
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, 72076, Germany
| | - Dirk Schwarzer
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, 72076, Germany
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, Gif-sur-Yvette Cedex, 91198, France
| | - Iris Finkemeier
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Muenster, Münster, 48149, Germany
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, Gif-sur-Yvette Cedex, 91198, France
| | - Ruediger Hell
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center, Heidelberg, 69120, Germany
| | - Markus Wirtz
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
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22
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Protein N-Terminal Acetylation: Structural Basis, Mechanism, Versatility, and Regulation. Trends Biochem Sci 2020; 46:15-27. [PMID: 32912665 DOI: 10.1016/j.tibs.2020.08.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/03/2020] [Accepted: 08/06/2020] [Indexed: 12/15/2022]
Abstract
N-terminal acetylation (NTA) is one of the most widespread protein modifications, which occurs on most eukaryotic proteins, but is significantly less common on bacterial and archaea proteins. This modification is carried out by a family of enzymes called N-terminal acetyltransferases (NATs). To date, 12 NATs have been identified, harboring different composition, substrate specificity, and in some cases, modes of regulation. Recent structural and biochemical analysis of NAT proteins allows for a comparison of their molecular mechanisms and modes of regulation, which are described here. Although sharing an evolutionarily conserved fold and related catalytic mechanism, each catalytic subunit uses unique elements to mediate substrate-specific activity, and use NAT-type specific auxiliary and regulatory subunits, for their cellular functions.
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23
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Deng S, Pan B, Gottlieb L, Petersson EJ, Marmorstein R. Molecular basis for N-terminal alpha-synuclein acetylation by human NatB. eLife 2020; 9:57491. [PMID: 32885784 PMCID: PMC7494357 DOI: 10.7554/elife.57491] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 09/03/2020] [Indexed: 12/20/2022] Open
Abstract
NatB is one of three major N-terminal acetyltransferase (NAT) complexes (NatA-NatC), which co-translationally acetylate the N-termini of eukaryotic proteins. Its substrates account for about 21% of the human proteome, including well known proteins such as actin, tropomyosin, CDK2, and α-synuclein (αSyn). Human NatB (hNatB) mediated N-terminal acetylation of αSyn has been demonstrated to play key roles in the pathogenesis of Parkinson's disease and as a potential therapeutic target for hepatocellular carcinoma. Here we report the cryo-EM structure of hNatB bound to a CoA-αSyn conjugate, together with structure-guided analysis of mutational effects on catalysis. This analysis reveals functionally important differences with human NatA and Candida albicans NatB, resolves key hNatB protein determinants for αSyn N-terminal acetylation, and identifies important residues for substrate-specific recognition and acetylation by NatB enzymes. These studies have implications for developing small molecule NatB probes and for understanding the mode of substrate selection by NAT enzymes.
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Affiliation(s)
- Sunbin Deng
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Buyan Pan
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States
| | - Leah Gottlieb
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Ronen Marmorstein
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
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24
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Armbruster L, Linster E, Boyer JB, Brünje A, Eirich J, Stephan I, Bienvenut WV, Weidenhausen J, Meinnel T, Hell R, Sinning I, Finkemeier I, Giglione C, Wirtz M. NAA50 Is an Enzymatically Active N α-Acetyltransferase That Is Crucial for Development and Regulation of Stress Responses. PLANT PHYSIOLOGY 2020; 183:1502-1516. [PMID: 32461302 PMCID: PMC7401105 DOI: 10.1104/pp.20.00222] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/15/2020] [Indexed: 05/11/2023]
Abstract
Nα-terminal acetylation (NTA) is a prevalent protein modification in eukaryotes. In plants, the biological function of NTA remains enigmatic. The dominant N-acetyltransferase (Nat) in Arabidopsis (Arabidopsis thaliana) is NatA, which cotranslationally catalyzes acetylation of ∼40% of the proteome. The core NatA complex consists of the catalytic subunit NAA10 and the ribosome-anchoring subunit NAA15. In human (Homo sapiens), fruit fly (Drosophila melanogaster), and yeast (Saccharomyces cerevisiae), this core NatA complex interacts with NAA50 to form the NatE complex. While in metazoa, NAA50 has N-acetyltransferase activity, yeast NAA50 is catalytically inactive and positions NatA at the ribosome tunnel exit. Here, we report the identification and characterization of Arabidopsis NAA50 (AT5G11340). Consistent with its putative function as a cotranslationally acting Nat, AtNAA50-EYFP localized to the cytosol and the endoplasmic reticulum but also to the nuclei. We demonstrate that purified AtNAA50 displays Nα-terminal acetyltransferase and lysine-ε-autoacetyltransferase activity in vitro. Global N-acetylome profiling of Escherichia coli cells expressing AtNAA50 revealed conservation of NatE substrate specificity between plants and humans. Unlike the embryo-lethal phenotype caused by the absence of AtNAA10 and AtNAA15, loss of NAA50 expression resulted in severe growth retardation and infertility in two Arabidopsis transfer DNA insertion lines (naa50-1 and naa50-2). The phenotype of naa50-2 was rescued by the expression of HsNAA50 or AtNAA50. In contrast, the inactive ScNAA50 failed to complement naa50-2 Remarkably, loss of NAA50 expression did not affect NTA of known NatA substrates and caused the accumulation of proteins involved in stress responses. Overall, our results emphasize a relevant role of AtNAA50 in plant defense and development, which is independent of the essential NatA activity.
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Affiliation(s)
- Laura Armbruster
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Eric Linster
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Jean-Baptiste Boyer
- Université Paris-Saclay, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Institute for Integrative Biology of the Cell, 91198 Gif-sur-Yvette, France
| | - Annika Brünje
- Institute for Plant Biology and Biotechnology, University of Münster, Muenster 48149, Germany
| | - Jürgen Eirich
- Institute for Plant Biology and Biotechnology, University of Münster, Muenster 48149, Germany
| | - Iwona Stephan
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Willy V Bienvenut
- Université Paris-Saclay, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Institute for Integrative Biology of the Cell, 91198 Gif-sur-Yvette, France
| | | | - Thierry Meinnel
- Université Paris-Saclay, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Institute for Integrative Biology of the Cell, 91198 Gif-sur-Yvette, France
| | - Ruediger Hell
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Iris Finkemeier
- Institute for Plant Biology and Biotechnology, University of Münster, Muenster 48149, Germany
| | - Carmela Giglione
- Université Paris-Saclay, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Institute for Integrative Biology of the Cell, 91198 Gif-sur-Yvette, France
| | - Markus Wirtz
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
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25
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Bader I, McTiernan N, Darbakk C, Boltshauser E, Ree R, Ebner S, Mayr JA, Arnesen T. Severe syndromic ID and skewed X-inactivation in a girl with NAA10 dysfunction and a novel heterozygous de novo NAA10 p.(His16Pro) variant - a case report. BMC MEDICAL GENETICS 2020; 21:153. [PMID: 32698785 PMCID: PMC7374887 DOI: 10.1186/s12881-020-01091-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/12/2020] [Indexed: 01/20/2023]
Abstract
Background NAA10 is the catalytic subunit of the major N-terminal acetyltransferase complex NatA which acetylates almost half the human proteome. Over the past decade, many NAA10 missense variants have been reported as causative of genetic disease in humans. Individuals harboring NAA10 variants often display variable degrees of intellectual disability (ID), developmental delay, and cardiac anomalies. Initially, carrier females appeared to be oligo- or asymptomatic with X-inactivation pattern skewed towards the wild type allele. However, recently it has been shown that NAA10 variants can cause syndromic or non-syndromic intellectual disability in females as well. The impact of specific NAA10 variants and the X-inactivation pattern on the individual phenotype in females remains to be elucidated. Case presentation Here we present a novel de novo NAA10 (NM_003491.3) c.[47A > C];[=] (p.[His16Pro];[=]) variant identified in a young female. The 10-year-old girl has severely delayed motor and language development, disturbed behavior with hyperactivity and restlessness, moderate dilatation of the ventricular system and extracerebral CSF spaces. Her blood leukocyte X-inactivation pattern was skewed (95/5) towards the maternally inherited X-chromosome. Our functional study indicates that NAA10 p.(H16P) impairs NatA complex formation and NatA catalytic activity, while monomeric NAA10 catalytic activity appears to be intact. Furthermore, cycloheximide experiments show that the NAA10 H16P variant does not affect the cellular stability of NAA10. Discussion and conclusions We demonstrate that NAA10 p.(His16Pro) causes a severe form of syndromic ID in a girl most likely through impaired NatA-mediated Nt-acetylation of cellular proteins. X-inactivation analyses showed a skewed X-inactivation pattern in DNA from blood of the patient with the maternally inherited allele being preferentially methylated/inactivated.
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Affiliation(s)
- Ingrid Bader
- Einheit für Klinische Genetik, Universitätsklinik für Kinder- und Jugendheilkunde, Paracelsus Medizinische Universität, Müllner Hauptstraße 48, A-5020, Salzburg, Austria.
| | - Nina McTiernan
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | | | - Rasmus Ree
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Sabine Ebner
- Einheit für Klinische Genetik, Universitätsklinik für Kinder- und Jugendheilkunde, Paracelsus Medizinische Universität, Müllner Hauptstraße 48, A-5020, Salzburg, Austria
| | - Johannes A Mayr
- Children's Hospital, Paracelsus Medical University, Salzburg, Austria
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway.,Department of Biological Sciences, University of Bergen, Bergen, Norway.,Department of Surgery, Haukeland University Hospital, Bergen, Norway
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26
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Kung PP, Bingham P, Burke BJ, Chen Q, Cheng X, Deng YL, Dou D, Feng J, Gallego GM, Gehring MR, Grant SK, Greasley S, Harris AR, Maegley KA, Meier J, Meng X, Montano JL, Morgan BA, Naughton BS, Palde PB, Paul TA, Richardson P, Sakata S, Shaginian A, Sonnenburg WK, Subramanyam C, Timofeevski S, Wan J, Yan W, Stewart AE. Characterization of Specific N-α-Acetyltransferase 50 (Naa50) Inhibitors Identified Using a DNA Encoded Library. ACS Med Chem Lett 2020; 11:1175-1184. [PMID: 32550998 DOI: 10.1021/acsmedchemlett.0c00029] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 04/10/2020] [Indexed: 11/29/2022] Open
Abstract
Two novel compounds were identified as Naa50 binders/inhibitors using DNA-encoded technology screening. Biophysical and biochemical data as well as cocrystal structures were obtained for both compounds (3a and 4a) to understand their mechanism of action. These data were also used to rationalize the binding affinity differences observed between the two compounds and a MLGP peptide-containing substrate. Cellular target engagement experiments further confirm the Naa50 binding of 4a and demonstrate its selectivity toward related enzymes (Naa10 and Naa60). Additional analogs of inhibitor 4a were also evaluated to study the binding mode observed in the cocrystal structures.
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Affiliation(s)
- Pei-Pei Kung
- Worldwide Research and Development, Pfizer Inc., 10770 Science Center Drive, San Diego, California 92121, United States
| | - Patrick Bingham
- Worldwide Research and Development, Pfizer Inc., 10770 Science Center Drive, San Diego, California 92121, United States
| | - Benjamin J. Burke
- Worldwide Research and Development, Pfizer Inc., 10770 Science Center Drive, San Diego, California 92121, United States
| | - Qiuxia Chen
- HitGen Inc., Building 6, No.8, Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu, Sichuan 610200, P.R. China
| | - Xuemin Cheng
- HitGen Inc., Building 6, No.8, Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu, Sichuan 610200, P.R. China
| | - Ya-Li Deng
- Worldwide Research and Development, Pfizer Inc., 10770 Science Center Drive, San Diego, California 92121, United States
| | - Dengfeng Dou
- HitGen Inc., Building 6, No.8, Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu, Sichuan 610200, P.R. China
| | - Junli Feng
- Worldwide Research and Development, Pfizer Inc., 10770 Science Center Drive, San Diego, California 92121, United States
| | - Gary M. Gallego
- Worldwide Research and Development, Pfizer Inc., 10770 Science Center Drive, San Diego, California 92121, United States
| | - Michael R. Gehring
- Worldwide Research and Development, Pfizer Inc., 10770 Science Center Drive, San Diego, California 92121, United States
| | - Stephan K. Grant
- Worldwide Research and Development, Pfizer Inc., 10770 Science Center Drive, San Diego, California 92121, United States
| | - Samantha Greasley
- Worldwide Research and Development, Pfizer Inc., 10770 Science Center Drive, San Diego, California 92121, United States
| | - Anthony R. Harris
- Worldwide Research and Development, Pfizer Inc., 10770 Science Center Drive, San Diego, California 92121, United States
| | - Karen A. Maegley
- Worldwide Research and Development, Pfizer Inc., 10770 Science Center Drive, San Diego, California 92121, United States
| | - Jordan Meier
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Xiaoyun Meng
- HitGen Inc., Building 6, No.8, Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu, Sichuan 610200, P.R. China
| | - Jose L. Montano
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Barry A. Morgan
- HitGen Inc., Building 6, No.8, Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu, Sichuan 610200, P.R. China
- HitGen Pharmaceuticals Inc., PO Box 88240, Houston, Texas 77288, United States
| | - Brigitte S. Naughton
- Worldwide Research and Development, Pfizer Inc., 10770 Science Center Drive, San Diego, California 92121, United States
| | - Prakash B. Palde
- Worldwide Research and Development, Pfizer Inc., 10770 Science Center Drive, San Diego, California 92121, United States
| | - Thomas A. Paul
- Worldwide Research and Development, Pfizer Inc., 10770 Science Center Drive, San Diego, California 92121, United States
| | - Paul Richardson
- Worldwide Research and Development, Pfizer Inc., 10770 Science Center Drive, San Diego, California 92121, United States
| | - Sylvie Sakata
- Worldwide Research and Development, Pfizer Inc., 10770 Science Center Drive, San Diego, California 92121, United States
| | - Alex Shaginian
- HitGen Inc., Building 6, No.8, Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu, Sichuan 610200, P.R. China
| | - William K. Sonnenburg
- HitGen Inc., Building 6, No.8, Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu, Sichuan 610200, P.R. China
| | - Chakrapani Subramanyam
- Worldwide Research and Development, Pfizer Inc., 10770 Science Center Drive, San Diego, California 92121, United States
| | - Sergei Timofeevski
- Worldwide Research and Development, Pfizer Inc., 10770 Science Center Drive, San Diego, California 92121, United States
| | - Jinqiao Wan
- HitGen Inc., Building 6, No.8, Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu, Sichuan 610200, P.R. China
| | - Wen Yan
- Worldwide Research and Development, Pfizer Inc., 10770 Science Center Drive, San Diego, California 92121, United States
| | - Albert E. Stewart
- Worldwide Research and Development, Pfizer Inc., 10770 Science Center Drive, San Diego, California 92121, United States
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27
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Deng S, McTiernan N, Wei X, Arnesen T, Marmorstein R. Molecular basis for N-terminal acetylation by human NatE and its modulation by HYPK. Nat Commun 2020; 11:818. [PMID: 32042062 PMCID: PMC7010799 DOI: 10.1038/s41467-020-14584-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 01/18/2020] [Indexed: 01/04/2023] Open
Abstract
The human N-terminal acetyltransferase E (NatE) contains NAA10 and NAA50 catalytic, and NAA15 auxiliary subunits and associates with HYPK, a protein with intrinsic NAA10 inhibitory activity. NatE co-translationally acetylates the N-terminus of half the proteome to mediate diverse biological processes, including protein half-life, localization, and interaction. The molecular basis for how NatE and HYPK cooperate is unknown. Here, we report the cryo-EM structures of human NatE and NatE/HYPK complexes and associated biochemistry. We reveal that NAA50 and HYPK exhibit negative cooperative binding to NAA15 in vitro and in human cells by inducing NAA15 shifts in opposing directions. NAA50 and HYPK each contribute to NAA10 activity inhibition through structural alteration of the NAA10 substrate-binding site. NAA50 activity is increased through NAA15 tethering, but is inhibited by HYPK through structural alteration of the NatE substrate-binding site. These studies reveal the molecular basis for coordinated N-terminal acetylation by NatE and HYPK.
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Affiliation(s)
- Sunbin Deng
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nina McTiernan
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Xuepeng Wei
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway.,Department of Biological Sciences, University of Bergen, Bergen, Norway.,Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - Ronen Marmorstein
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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28
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Lyon GJ. From Molecular Understanding to Organismal Biology of N-Terminal Acetyltransferases. Structure 2019; 27:1053-1055. [PMID: 31269458 DOI: 10.1016/j.str.2019.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In this issue of Structure, Deng et al. (2019) determine the structure of the yeast N-terminal acetyltransferases Naa10 and Naa50 in complex with Naa15 and demonstrate that Naa50 has negligible catalytic activity on its own but modulates Naa10/Naa15. This study provides insights into mechanisms involving amino-terminal acetylation of proteins.
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Affiliation(s)
- Gholson J Lyon
- Institute for Basic Research in Developmental Disabilities (IBR), Staten Island, NY 10314, USA; Biology PhD Program, The Graduate Center, The City University of New York, NY 10016, USA.
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29
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Gottlieb L, Marmorstein R. Biochemical and structural analysis of N-terminal acetyltransferases. Methods Enzymol 2019; 626:271-299. [PMID: 31606079 DOI: 10.1016/bs.mie.2019.07.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
N-terminal acetylation is a co- and post-translational modification catalyzed by the conserved N-terminal acetyltransferase (NAT) family of enzymes. A majority of the human proteome is modified by the human NATs (NatA-F and H), which are minimally composed of a catalytic subunit and as many as two auxiliary subunits. Together, NATs specifically regulate many cellular functions by influencing protein activities such as their degradation, membrane targeting, and protein-protein interactions. This chapter will describe methods developed for their preparation, and their biochemical and structural characterization. This will include methodologies for expression and purification of recombinant NAT protein, kinetic assays, biochemical and biophysical assays, and strategies for structural studies.
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Affiliation(s)
- Leah Gottlieb
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Ronen Marmorstein
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
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